A Comparison of Efficiency Parameters of SRAP and ISSR Markers in Revealing Variation in Allium Germplasm

In this study, we present the first-ever comparison of the effectiveness of SRAP and ISSR markers on three Allium species. In addition, to visualize the results of each dataset in a simpler way, the Fruchterman–Reingold algorithm was used to generate a link graph and neighbor-joining methods were used to obtain a phylogenetic tree. The genetic similarity matrices were compared using the Mantel test. Primers generated 59 ISSR and 72 SRAP fragments. There was no statistically significant difference between the polymorphism information content of the marker sets. In terms of the effective multiplex ratio, SRAP markers were higher than ISSR markers, with values of 6.700 for garlic, 6.400 for onion, and 5.800 for leek (3.490, 4.316, and 2.573, respectively). Similarly, the marker index was calculated as 2.820, 3.056, and 2.505 for SRAP and 1.903, 1.523, and 1.050 for ISSR in onion, garlic, and leek species, respectively. The highest value regarding cophenetic correlation coefficients was obtained from the Jaccard method. According to the neighbor-joining method, the tree drawn using SRAP and ISSR data together shows a more distinct hierarchical structure of genotypes. The results obtained proved that SRAPs have higher values in terms of sign efficiency criteria, but they are not sufficient for the homogeneous grouping of different Allium species.